In this proposal, we describe a novel therapeutic strategy for the treatment of cancer based on the hypothesis that the higher frequency of loss of heterozygosity (LOH) in cancer cells renders them more susceptible to drugs that target the products of the remaining alleles. Our goal is to develop allele-specific inhibitors of essential genes that are heterozygous in normal cells by reduced to hemizygosity in cancer cells. We expect the allele-specific inhibitor to be sensitively toxic to cancer cells, which express only the targeted allele. In Phase I, we will evaluate the potential of human glutamyl-prolyl tRNA synthetase (EPRS) as a target for developing allele-specific inhibitors. The human EPRS gene is subject to LOH in multiple cancer types. Variagenics has identified a common amino acid polymorphism in the prolyl domain. To determine whether the polymorphism is on the surface of the enzyme and therefore accessible to small molecules, we will map accessibility using chemical modification reagents. Assay of Michaelis- Menten kinetic constants for each of the three substrates (ATP, proline, and tRNA pro) combined with structure/function studies will determine if the polymorphism lies in a domain required for activity. These studies will lay the foundation of the identification of allele-specific drugs in Phase II. PROPOSED COMMERCIAL APPLICATION: Effective therapy is not currently available for most solid tumors. Variagenics is developing a new class of cancer-specific therapeutic inhibitors that exploit allele loss in cancer cells. Allele-specific inhibitors of glutamyl-prolyl tRNA synthetase would be useful in treating breast, lung, prostate, and esophageal cancers, all of which have 20 to 50% allele loss at the EPRS gene locus.